Hands-on Workshop on Computational Biophysics 2019
Dates: May 13 - 17, 2019
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA
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This workshop covered a wide range of physical models and computational approaches for the simulation of biological systems at multiple scales, using cutting edge technology including ProDy, NAMD, VMD, iGNM and ANM. The course was based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.
The workshop was presented by members of the Theoretical and Computational Biophysics Group (www.ks.uiuc.edu) from the University of Illinois at Urbana-Champaign (UIUC) and the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh.
The workshop was designed for students and researchers in computational and/or biophysical fields who sought to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning were followed by hands-on computer labs in the afternoon in which students set up and ran simulations.
Agenda
See the workshop agenda.
Workshop Instructors:
Ivet Bahar (University of Pittsburgh)
Emad Tajkhorshid (UIUC)
João Ribeiro (UIUC)
Pemra Doruker (University of Pittsburgh)
Mariano Spivak (UIUC)
Assistant Instructors:
Burak Kaynak (University of Pittsburgh)
James Kreiger (University of Pittsburgh)
Hongchun Li (University of Pittsburgh)
JiYoung Lee (University of Pittsburgh)
Luca Ponzoni (University of Pittsburgh)
Soumyo Sen (UIUC)
She (John) Zhang (Carnegie Mellon University/University of Pittsburgh)
Yan Zhang (Carnegie Mellon University/University of Pittsburgh)